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García-Estrada DA, Selem-Mojica N, Martínez-Hernández A, Lara-Reyna J, Dávila-Ramos S, Verdel-Aranda K. Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era. BMC Microbiol 2024; 24:376. [PMID: 39342129 PMCID: PMC11437969 DOI: 10.1186/s12866-024-03523-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/16/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics. RESULTS Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria. CONCLUSION This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.
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Affiliation(s)
- David Alberto García-Estrada
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Nelly Selem-Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México (UNAM), Morelia, Michoacán, Mexico
| | | | - Joel Lara-Reyna
- Colegio de Postgraduados Campus Campeche, Sihochac, Champotón, Campeche, Mexico.
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico
| | - Karina Verdel-Aranda
- Conahcyt-Colegio de Postgraduados Campus Campeche, Sihochac, Champotón, Campeche, Mexico.
- Present address: Tecnológico Nacional de México-Instituto Tecnológico de Chiná, Chiná, Campeche, Mexico.
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Banerjee G, Papri SR, Banerjee P. Protocol for the construction and functional profiling of metagenome-assembled genomes for microbiome analyses. STAR Protoc 2024; 5:103167. [PMID: 38954516 PMCID: PMC11263634 DOI: 10.1016/j.xpro.2024.103167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/08/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Constructing metagenome-assembled genomes (MAGs) from complex metagenomic samples involves a series of bioinformatics operations, each requiring deep bioinformatics knowledge. Here, we present a protocol for constructing MAGs and conducting functional profiling to address biological questions. We describe steps for system configuration, data downloads, read processing, removal of human DNA contamination, metagenomic assembly, and statistical quality assessment of the final assembly. Additionally, we detail procedures for the construction and refinement of MAGs, as well as the functional profiling of MAGs.
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Affiliation(s)
- Goutam Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Suraya Rahman Papri
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Tomazelli D, Klauberg-Filho O, Mendes LW, Goss-Souza D. The impact of land-use changes and management intensification on bacterial communities in the last decade: a review. Appl Environ Microbiol 2024; 90:e0030924. [PMID: 38874336 PMCID: PMC11267915 DOI: 10.1128/aem.00309-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024] Open
Abstract
In the last decade, advances in soil bacterial ecology have contributed to increasing agricultural production. Brazil is the world leading agriculture producer and leading soil biodiversity reservoir. Meanwhile, there is still a significant gap in the knowledge regarding the soil microscopic life and its interactions with agricultural practices, and the replacement of natural vegetation by agroecosystems is yet to be unfolded. Through high throughput DNA sequencing, scientists are now exploring the complexity of soil bacterial communities and their relationship with soil and environmental characteristics. This study aimed to investigate the progress of bacterial ecology studies in Brazil over the last 10 years, seeking to understand the effect of the conversion of natural vegetation in agricultural systems on the diversity and structure of the soil microbial communities. We conducted a systematic search for scientific publication databases. Our systematic search has matched 62 scientific articles from three different databases. Most of the studies were placed in southeastern and northern Brazil, with no records of studies about microbial ecology in 17 out of 27 Brazilian states. Out of the 26 studies that examined the effects of replacing natural vegetation with agroecosystems, most authors concluded that changes in soil pH and vegetation cover replacement were the primary drivers of shifts in microbial communities. Understanding the ecology of the bacteria inhabiting Brazilian soils in agroecosystems is paramount for developing more efficient soil management strategies and cleaner agricultural technologies.
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Affiliation(s)
- Daniela Tomazelli
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, Santa Catarina, Brazil
| | - Osmar Klauberg-Filho
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, Santa Catarina, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Dennis Goss-Souza
- College of Agronomy, Federal Institute of Paraná, Palmas, Paraná, Brazil
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4
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Chang T, Gavelis GS, Brown JM, Stepanauskas R. Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton. MICROBIOME 2024; 12:126. [PMID: 39010229 PMCID: PMC11247762 DOI: 10.1186/s40168-024-01848-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/28/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are the predominant sources of information about the coding potential of uncultured microbial lineages, but their strengths and limitations remain poorly understood. Here, we performed a direct comparison of two previously published collections of thousands of SAGs and MAGs obtained from the same, global environment. RESULTS We found that SAGs were less prone to chimerism and more accurately reflected the relative abundance and the pangenome content of microbial lineages inhabiting the epipelagic of the tropical and subtropical ocean, as compared to MAGs. SAGs were also better suited to link genome information with taxa discovered through 16S rRNA amplicon analyses. Meanwhile, MAGs had the advantage of more readily recovering genomes of rare lineages. CONCLUSIONS Our analyses revealed the relative strengths and weaknesses of the two most commonly used genome recovery approaches in environmental microbiology. These considerations, as well as the need for better tools for genome quality assessment, should be taken into account when designing studies and interpreting data that involve SAGs or MAGs. Video Abstract.
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Affiliation(s)
- Tianyi Chang
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Gregory S Gavelis
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
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5
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Chaudhari NM, Pérez-Carrascal OM, Overholt WA, Totsche KU, Küsel K. Genome streamlining in Parcubacteria transitioning from soil to groundwater. ENVIRONMENTAL MICROBIOME 2024; 19:41. [PMID: 38902796 PMCID: PMC11188291 DOI: 10.1186/s40793-024-00581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics. RESULTS Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer. CONCLUSIONS Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.
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Affiliation(s)
- Narendrakumar M Chaudhari
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany
| | - Olga M Pérez-Carrascal
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Will A Overholt
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geowissenschaften, Friedrich-Schiller-Universität Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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6
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Feng X, Li H. Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies. Genome Biol 2024; 25:92. [PMID: 38605401 PMCID: PMC11007910 DOI: 10.1186/s13059-024-03234-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/29/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them. RESULTS Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins. CONCLUSIONS Our work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.
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Affiliation(s)
- Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA.
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Qiu Z, Yuan L, Lian CA, Lin B, Chen J, Mu R, Qiao X, Zhang L, Xu Z, Fan L, Zhang Y, Wang S, Li J, Cao H, Li B, Chen B, Song C, Liu Y, Shi L, Tian Y, Ni J, Zhang T, Zhou J, Zhuang WQ, Yu K. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nat Commun 2024; 15:2179. [PMID: 38467684 PMCID: PMC10928208 DOI: 10.1038/s41467-024-46539-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
| | - Li Yuan
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
| | - Bin Lin
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
| | - Jie Chen
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Liyu Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Zheng Xu
- Southern University of Sciences and Technology Yantian Hospital, Shenzhen, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Yunzeng Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China
| | - Junyi Li
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Huiluo Cao
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Bing Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Wuhan Benagen Technology Co., Ltd, Wuhan, China
| | - Yongxin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lili Shi
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yonghong Tian
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Jinren Ni
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - Tong Zhang
- Department of Civil Engineering, University of Hong Kong, Hong Kong, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wei-Qin Zhuang
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Auckland, Auckland, New Zealand
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China.
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Wang L, Zhang H, Xu C, Yuan J, Xu X, Wang J, Zhang Y. Long-term nitrogen fertilization and sweetpotato cultivation in the wheat-sweetpotato rotation system decrease alkaline phosphomonoesterase activity by regulating soil phoD-harboring bacteria communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165916. [PMID: 37524185 DOI: 10.1016/j.scitotenv.2023.165916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
The alkaline phosphomonoesterase (ALP)-harboring community (phoD-harboring community) plays a crucial role in the conversion of organic phosphorus (P) into available P (AP). However, the response mechanisms of phoD-harboring communities to fertilization strategies, crop types, and their interactions within the wheat-sweetpotato rotation are poorly understood. A nine-year field experiment of different fertilization strategies was established under the wheat-sweetpotato rotation. After harvesting the crop, we collected soil samples without fertilization (CK), inorganic NK fertilization (NK), inorganic NPK fertilization (NPK), and a combined application of inorganic NPK and organic fertilizer (NPKM). We employed high-throughput sequencing and enzymology techniques to analyze the composition and functional activity of phoD-harboring bacterial communities as well as their correlation with soil physicochemical properties. The results showed that long-term nitrogen (N) fertilization, especially inorganic N, significantly reduced soil pH and ALP activity while increasing AP compared with CK. The AP content in sweetpotato season was significantly higher than that in wheat season. Inorganic N fertilization dramatically reshaped the communities of phoD-harboring bacteria and decreased diversity. The phoD-harboring bacterial communities in sweetpotato season were significantly different from those in wheat season. The N fertilization significantly reduced the relative abundance of Acuticoccus, Methylibium, Rhizobacter, and Roseivivax, which was positively correlated with ALP activity. These groups in sweetpotato season decreased significantly compared with wheat season. A structural equation model indicates that pH and AP play a significant role in regulating the phoD-harboring bacteria communities, ALP activity, and their interactions. We demonstrate that fertilization strategies and crop types have a substantial impact on the phoD-harboring bacteria communities and functions, which are closely linked to soil pH and AP levels. Our study highlights the detrimental effects of soil acidification resulting from inorganic N fertilization on P-cycling bacterial communities and functions. However, the combination of inorganic and organic fertilizer can mitigate these adverse effects.
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Affiliation(s)
- Lei Wang
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hui Zhang
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu University, Zhenjiang 212023, China
| | - Cong Xu
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu University, Zhenjiang 212023, China
| | - Jie Yuan
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xianjü Xu
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jidong Wang
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu University, Zhenjiang 212023, China.
| | - Yongchun Zhang
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu University, Zhenjiang 212023, China.
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Santana-Pereira ALR, Moen FS, Severance B, Liles MR. Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment. Front Microbiol 2023; 14:1114548. [PMID: 37577441 PMCID: PMC10413278 DOI: 10.3389/fmicb.2023.1114548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Bacteria affiliated with the Candidate Phyla Radiation (CPR) are a hyper-diverse group of ultra-small bacteria with versatile yet sparse metabolisms. However, most insights into this group come from a surprisingly small number of environments, and recovery of CPR bacteria from soils has been hindered due to their extremely low abundance within complex microbial assemblages. In this study we enriched soil samples from 14 different soil fertility treatments for ultra-small (<0.45 μm) bacteria in order to study rare soil CPR. 42 samples were sequenced, enabling the reconstruction of 27 quality CPR metagenome-assembled genomes (MAGs) further classified as Parcubacteria/Paceibacteria, Saccharibacteria/Saccharimonadia and ABY1, in addition to representative genomes from Gemmatimonadetes, Dependentiae and Chlamydae phyla. These genomes were fully annotated and used to reconstruct the CPR community across all 14 plots. Additionally, for five of these plots, the entire microbiota was reconstructed using 16S amplification, showing that specific soil CPR may form symbiotic relationships with a varied and circumstantial range of hosts. Cullars CPR had a prevalence of enzymes predicted to degrade plant-derived carbohydrates, which suggests they have a role in plant biomass degradation. Parcubacteria appear to be more apt at microfauna necromass degradation. Cullars Saccharibacteria and a Parcubacteria group were shown to carry a possible aerotolerance mechanism coupled with potential for aerobic respiration, which appear to be a unique adaptation to the oxic soil environment. Reconstruction of CPR communities across treatment plots showed that they were not impacted by changes in nutrient levels or microbiota composition, being only impacted by extreme conditions, causing some CPR to dominate the community. These findings corroborate the understanding that soil-dwelling CPR bacteria have a very broad symbiont range and have metabolic capabilities associated to soil environments which allows them to scavenge resources and form resilient communities. The contributions of these microbial dark matter species to soil ecology and plant interactions will be of significant interest in future studies.
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Affiliation(s)
| | | | | | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
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10
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Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA.
- Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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11
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Li T, Yin Y. Critical assessment of pan-genomic analysis of metagenome-assembled genomes. Brief Bioinform 2022; 23:6702672. [PMID: 36124775 PMCID: PMC9677465 DOI: 10.1093/bib/bbac413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 12/30/2022] Open
Abstract
Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.
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Affiliation(s)
- Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, 68508, USA
| | - Yanbin Yin
- Corresponding author. Yanbin Yin, Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68508, USA. Tel.: +1-402-472-4303; E-mail:
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12
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Lyu Q, Luo Y, Liu S, Zhang Y, Li X, Hou G, Chen G, Zhao K, Fan C, Li X. Forest gaps alter the soil bacterial community of weeping cypress plantations by modulating the understory plant diversity. FRONTIERS IN PLANT SCIENCE 2022; 13:920905. [PMID: 36061809 PMCID: PMC9437579 DOI: 10.3389/fpls.2022.920905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Weeping cypress is an endemic tree species that is widely planted in China, and the simple stand structure and fragile ecosystem of its plantation are common issues. Exploring the effect of different gap sizes on the soil bacterial community structure of weeping cypress plantations can provide a theoretical basis for the near-natural management of forest plantations. We, therefore, constructed three kinds of forest gaps with different sizes in weeping cypress plantations, namely, small (50-100 m2), medium (100-200 m2), and large gaps (400-667 m2), for identifying the key factors that affect soil bacterial communities following the construction of forest gaps. The results suggested that the herb layer was more sensitive than the shrub layer, while the Simpson, Shannon, and richness indices of the herb layer in plots with gaps were significantly higher than those of designated sampling plots without any gaps (CK). The presence of large gaps significantly increased the understory plant diversity and the Shannon and Simpson indices of the soil bacterial alpha diversity. There were obvious changes in the community composition of soil bacteria following the construction of forest gaps. The dominant bacterial phyla, orders, and functions were similar across the plots with different gap sizes. Of the indicator bacterial species, the abundance of the nitrogen-fixing bacteria, Lysobacter_ yangpyeongensis, and Ensifer_meliloti, was significantly different across plots with different gap sizes and accounted for a large proportion of the bacterial population of plots with medium and large gaps. The understory plant diversity was mostly related to the soil bacterial community than to other soil factors. The results of structural equation modeling indicated that the understory plant diversity was the most important environmental factor in driving the composition and diversity of bacterial communities. The construction of forest gaps significantly improved the understory plant diversity, physicochemical properties of the soil, and bacterial diversity in weeping cypress plantations, and the results of the comprehensive evaluation were in the order: large gaps > small gaps > medium gaps > CK. Our results suggested that large gaps are beneficial for the diversity of above-ground plant communities and underground soil bacterial communities.
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Affiliation(s)
- Qian Lyu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yan Luo
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Size Liu
- Sichuan Academy of Forestry, Chengdu, China
| | - Yan Zhang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Xiangjun Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Guirong Hou
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Gang Chen
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Kuangji Zhao
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chuan Fan
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianwei Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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13
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Venturini AM, Gontijo JB, Mandro JA, Paula FS, Yoshiura CA, da França AG, Tsai SM. Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils. Microb Genom 2022; 8. [PMID: 35894927 PMCID: PMC9455692 DOI: 10.1099/mgen.0.000853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.
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Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, USA
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jéssica A Mandro
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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14
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Okeke ES, Olovo CV, Nkwoemeka NE, Okoye CO, Nwankwo CEI, Onu CJ. Microbial ecology and evolution is key to pandemics: using the coronavirus model to mitigate future public health challenges. Heliyon 2022; 8:e09449. [PMID: 35601228 PMCID: PMC9113781 DOI: 10.1016/j.heliyon.2022.e09449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/03/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022] Open
Abstract
Pandemics are global challenges that lead to total disruption of human activities. From the inception of human existence, all pandemics have resulted in loss of human lives. The coronavirus disease caused by SAR-CoV-2 began in China and is now at the global scale with an increase in mortality and morbidity. Numerous anthropogenic activities have been implicated in the emergence and severity of pandemics, including COVID-19. These activities cause changes in microbial ecology, leading to evolution due to mutation and recombination. This review hypothesized that an understanding of these anthropogenic activities would explain the dynamics of pandemics. The recent coronavirus model was used to study issues leading to microbial evolution, towards preventing future pandemics. Our review highlighted anthropogenic activities, including deforestation, mining activities, waste treatment, burning of fossil fuel, as well as international travels as drivers of microbial evolution leading to pandemics. Furthermore, human-animal interaction has also been implicated in pandemic incidents. Our study recommends substantial control of such anthropogenic activities as having been highlighted as ways to reduce the frequency of mutation, reduce pathogenic reservoirs, and the emergence of infectious diseases.
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Affiliation(s)
- Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences and Environmental Biology, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, 212013, PR China
| | - Chinasa Valerie Olovo
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University Zhenjiang, 212013, Jiangsu, PR China
| | - Ndidi Ethel Nkwoemeka
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
| | - Charles Obinwanne Okoye
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Biofuels Institute, School of Environment and Safety Engineering Jiangsu University, Zhenjiang, 212013, China
| | - Chidiebele Emmanuel Ikechukwu Nwankwo
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
| | - Chisom Joshua Onu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
- Department of Biological Sciences, College of Liberal Arts and Sciences, Detroit, Michigan, 48202, USA
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15
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Mathieu A, Leclercq M, Sanabria M, Perin O, Droit A. Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation. Front Microbiol 2022; 13:811495. [PMID: 35359727 PMCID: PMC8964132 DOI: 10.3389/fmicb.2022.811495] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
Shotgun sequencing of environmental DNA (i.e., metagenomics) has revolutionized the field of environmental microbiology, allowing the characterization of all microorganisms in a sequencing experiment. To identify the microbes in terms of taxonomy and biological activity, the sequenced reads must necessarily be aligned on known microbial genomes/genes. However, current alignment methods are limited in terms of speed and can produce a significant number of false positives when detecting bacterial species or false negatives in specific cases (virus, plasmids, and gene detection). Moreover, recent advances in metagenomics have enabled the reconstruction of new genomes using de novo binning strategies, but these genomes, not yet fully characterized, are not used in classic approaches, whereas machine and deep learning methods can use them as models. In this article, we attempted to review the different methods and their efficiency to improve the annotation of metagenomic sequences. Deep learning models have reached the performance of the widely used k-mer alignment-based tools, with better accuracy in certain cases; however, they still must demonstrate their robustness across the variety of environmental samples and across the rapid expansion of accessible genomes in databases.
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Affiliation(s)
- Alban Mathieu
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, QC, Canada
| | - Mickael Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, QC, Canada
| | | | - Olivier Perin
- Digital Sciences Department, L'Oréal Advanced Research, Aulnay-sous-Bois, France
| | - Arnaud Droit
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, QC, Canada
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16
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Fiard M, Cuny P, Sylvi L, Hubas C, Jézéquel R, Lamy D, Walcker R, El Houssainy A, Heimbürger-Boavida LE, Robinet T, Bihannic I, Gilbert F, Michaud E, Dirberg G, Militon C. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150667. [PMID: 34599952 DOI: 10.1016/j.scitotenv.2021.150667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cédric Hubas
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Dominique Lamy
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France; Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), Sorbonne Université, Univ Paris Est Créteil, IRD, CNRS, INRA, 4 place Jussieu, 75005 Paris, France.
| | - Romain Walcker
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Amonda El Houssainy
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | | | - Tony Robinet
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Franck Gilbert
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Rokubacteria in Northern Peatlands: Habitat Preferences and Diversity Patterns. Microorganisms 2021; 10:microorganisms10010011. [PMID: 35056460 PMCID: PMC8780371 DOI: 10.3390/microorganisms10010011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands.
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18
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Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil. mSphere 2021; 6:e0008521. [PMID: 34468166 PMCID: PMC8550312 DOI: 10.1128/msphere.00085-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several 13C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily 13C-labeled bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Stable-isotope-informed, genome-resolved metagenomics indicated that phage can be important agents of turnover of plant-derived carbon in soil. IMPORTANCE Plants grow in intimate association with soil microbial communities; these microbes can facilitate the availability of essential resources to plants. Thus, plant productivity commonly depends on interactions with rhizosphere bacteria, viruses, and eukaryotes. Our work is significant because we identified the organisms that took up plant-derived organic C in rhizosphere soil and determined that many of the active bacteria are plant pathogens or can impact plant growth via hormone modulation. Further, by showing that bacteriophage accumulate CO2-derived carbon, we demonstrated their vital roles in redistribution of plant-derived C into the soil environment through bacterial cell lysis. The use of stable-isotope probing (SIP) to identify consumption (or lack thereof) of root-derived C by key microbial community members within highly complex microbial communities opens the way for assessing manipulations of bacteria and phage with potentially beneficial and detrimental traits, ultimately providing a path to improved plant health and soil carbon storage.
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Durrer A, Gumiere T, Rumenos Guidetti Zagatto M, Petry Feiler H, Miranda Silva AM, Henriques Longaresi R, Homma SK, Cardoso EJBN. Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields. PeerJ 2021; 9:e11985. [PMID: 34631309 PMCID: PMC8465994 DOI: 10.7717/peerj.11985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 07/26/2021] [Indexed: 01/04/2023] Open
Abstract
Background The importance of organic farming has increased through the years to promote food security allied with minimal harm to the ecosystem. Besides the environmental benefits, a recurring problem associated with organic management is the unsatisfactory yield. A possible solution may rely on the soil microbiome, which presents a crucial role in the soil system. Here, we aimed to evaluate the soil bacterial community structure and composition under organic and conventional farming, considering the tropical climate and tropical soil. Methodology Our organic management treatments were composed by composted poultry manure and green manure with Bokashi. Both organic treatments were based on low nitrogen inputs. We evaluated the soil bacterial community composition by high-throughput sequencing of 16S rRNA genes, soil fertility, and soil enzyme activity in two organic farming systems, one conventional and the last transitional from conventional to organic. Results We observed that both organic systems evaluated in this study, have higher yield than the conventional treatment, even in a year with drought conditions. These yield results are highly correlated with changes in soil chemical properties and enzymatic activity. The attributes pH, Ca, P, alkaline phosphatase, and β- glucosidase activity are positively correlated with organic systems, while K and Al are correlated with conventional treatment. Also, our results show in the organic systems the changes in the soil bacteria community, being phyla Acidobacteria, Firmicutes, Nitrospirae, and Rokubacteria the most abundant. These phyla were correlated with soil biochemical changes in the organic systems, helping to increase crop yields. Conclusion Different organic management systems, (the so-called natural and organic management systems, which use distinct organic sources), shift the soil bacterial community composition, implying changes in their functionalities. Also, our results contributed to the identification of target bacterial groups and changes in soil chemical properties and enzymatic activity in a trophic organic farming system, which may contribute to higher crop yields.
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Affiliation(s)
- Ademir Durrer
- Soil Science Department/ Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Thiago Gumiere
- Department of Soil and Agricultural Engineering, Laval University, Quebec City, Canada, Canada
| | | | - Henrique Petry Feiler
- Soil Science Department/ Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Antonio Marcos Miranda Silva
- Soil Science Department/ Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | | | - Elke J B N Cardoso
- Soil Science Department/ Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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20
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Ritter CD, Forster D, Azevedo JAR, Antonelli A, Nilsson RH, Trujillo ME, Dunthorn M. Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding. MICROBIAL ECOLOGY 2021; 82:746-760. [PMID: 33604703 PMCID: PMC8463405 DOI: 10.1007/s00248-021-01719-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (várzeas) or by unfertile black waters (igapós), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian microorganism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region.
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Affiliation(s)
- Camila Duarte Ritter
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83, D-45141, Essen, Germany.
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Josue A R Azevedo
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, 69060-000, Brazil
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
- Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Micah Dunthorn
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83, D-45141, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
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21
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Jouffret V, Miotello G, Culotta K, Ayrault S, Pible O, Armengaud J. Increasing the power of interpretation for soil metaproteomics data. MICROBIOME 2021; 9:195. [PMID: 34587999 PMCID: PMC8482631 DOI: 10.1186/s40168-021-01139-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/29/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Soil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is usually performed using metagenomic sequences acquired for the same sample. However, such hugely diverse metagenomic datasets are difficult to assemble; in parallel, theoretical proteomes from isolates available in generic databases are of high quality. Both these factors advocate for the use of theoretical proteomes in metaproteomics interpretation pipelines. Here, we examined a number of database construction strategies with a view to increasing the outputs of metaproteomics studies performed on soil samples. RESULTS The number of peptide-spectrum matches was found to be of comparable magnitude when using public or sample-specific metagenomics-derived databases. However, numbers were significantly increased when a combination of both types of information was used in a two-step cascaded search. Our data also indicate that the functional annotation of the metaproteomics dataset can be maximized by using a combination of both types of databases. CONCLUSIONS A two-step strategy combining sample-specific metagenome database and public databases such as the non-redundant NCBI database and a massive soil gene catalog allows maximizing the metaproteomic interpretation both in terms of ratio of assigned spectra and retrieval of function-derived information. Video abstract.
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Affiliation(s)
- Virginie Jouffret
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
- Laboratoire des Sciences et de l'Environnement (LSCE-IPSL), UMR 8212 (CEA/CNRS/UVSQ), CEA Saclay, Université Paris-Saclay, Orme des Merisiers, F-91191, Gif-sur-Yvette, France
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, F-30207, Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
| | - Karen Culotta
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
| | - Sophie Ayrault
- Laboratoire des Sciences et de l'Environnement (LSCE-IPSL), UMR 8212 (CEA/CNRS/UVSQ), CEA Saclay, Université Paris-Saclay, Orme des Merisiers, F-91191, Gif-sur-Yvette, France
| | - Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200, Bagnols-sur-Cèze, France.
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22
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Zhang H, Li S, Zheng X, Zhang J, Bai N, Zhang H, Lv W. Effects of Biogas Slurry Combined With Chemical Fertilizer on Soil Bacterial and Fungal Community Composition in a Paddy Field. Front Microbiol 2021; 12:655515. [PMID: 34526972 PMCID: PMC8435896 DOI: 10.3389/fmicb.2021.655515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
The application of biogas slurry and chemical fertilizer in paddy fields can be a practical method to reduce the environmental risk and utilize the nutrients of biogas slurry. The responses of bacterial and fungal communities to the application of biogas slurry and chemical fertilizer are important reflections of the quality of the ecological environment. In this study, based on a 3-year field experiment with different ratios of biogas slurry and chemical fertilizer (applying the same pure nitrogen amount), the Illumina MiSeq platform was used to investigate the bacterial and fungal community diversity and composition in paddy soil. Our results revealed that compared with the observations under regular chemical fertilization, on the basis of stable paddy yield, the application of biogas slurry combined with chemical fertilizer significantly enhanced the soil nutrient availability and bacterial community diversity and reduced the fungal community diversity. Dissolved organic carbon (DOC), DOC/SOC (soil organic carbon), available nitrogen (AN) and available phosphorus (AP) were positively correlated with the bacterial community diversity, but no soil property was significantly associated with the fungal community. The bacterial community was primarily driven by the application of biogas slurry combined with chemical fertilizer (40.78%), while the fungal community was almost equally affected by the addition of pure biogas slurry, chemical fertilizer and biogas slurry combined with chemical fertilizer (25.65–28.72%). Biogas slurry combined with chemical fertilizer significantly enriched Proteobacteria, Acidobacteria, Planctomycetes, Rokubacteria, and Ascomycota and depleted Chloroflexi, Bacteroidetes, Crenarchaeota, Basidiomycota, and Glomeromycota. The observation of the alteration of some bacteria- and fungus-specific taxa provides insights for the proper application of biogas slurry combined with chemical fertilizer, which has the potential to promote crop growth and inhibit pathogens.
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Affiliation(s)
- Hanlin Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, China
| | - Shuangxi Li
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, China
| | - Xianqing Zheng
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, China
| | - Juanqin Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, China
| | - Naling Bai
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, China
| | - Haiyun Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, China
| | - Weiguang Lv
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, China
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23
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Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities. mSystems 2021; 6:e0120520. [PMID: 34402646 PMCID: PMC8407418 DOI: 10.1128/msystems.01205-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems but are rarely detected in soil. We concentrated particles of less than 0.2 μm in size from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in largely oxic environments such as soil. We recovered a diversity of CPR bacterial and some archaeal sequences but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms rarely reported in soil, as well as Saccharibacteria, Parcubacteria, and Microgenomates. CPR and archaea of the phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) were enriched 100- to 1,000-fold compared to that in bulk soil, in which we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also harbor ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We conclude that CPR bacteria and DPANN archaea are part of the rare soil biosphere and harbor unique metabolic platforms that potentially evolved to live symbiotically under relatively oxic conditions. IMPORTANCE Here, we investigated overlooked microbes in soil, Candidate Phyla Radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes. We found that some of these predicted symbionts, which have been largely studied in anaerobic systems, have acquired aerobic capacity via lateral transfer that may enable adaptation to oxic soil environments. We estimate that there are approximately 1 to 100 cells of each of these lineages per gram of soil, highlighting that the approach provides a window into the rare soil biosphere and its associated genetic potential.
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24
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Eskov AK, Zverev AO, Abakumov EV. Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other. Microorganisms 2021; 9:microorganisms9051033. [PMID: 34064848 PMCID: PMC8150705 DOI: 10.3390/microorganisms9051033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 01/04/2023] Open
Abstract
Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils-deposits collected by the epiphytes-which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity.
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Affiliation(s)
- Alen K. Eskov
- Faculty of Biology, Lomonosov Moscow State University, 1–12 Leninskie Gory, 119991 Moscow, Russia
- Tzitzin Main Botanical Garden, Russian Academy of Sciences, 4 Botanicheskaya ul., 117628 Moscow, Russia
- Correspondence:
| | - Alexei O. Zverev
- Faculty of Biology, Saint-Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; (A.O.Z.); (E.V.A.)
- All-Russian Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, 196608 St. Petersburg, Russia
| | - Evgeny V. Abakumov
- Faculty of Biology, Saint-Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; (A.O.Z.); (E.V.A.)
- All-Russian Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, 196608 St. Petersburg, Russia
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25
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Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
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26
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Kroeger ME, Meredith LK, Meyer KM, Webster KD, de Camargo PB, de Souza LF, Tsai SM, van Haren J, Saleska S, Bohannan BJM, Rodrigues JLM, Berenguer E, Barlow J, Nüsslein K. Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon. THE ISME JOURNAL 2021; 15:658-672. [PMID: 33082572 PMCID: PMC8027882 DOI: 10.1038/s41396-020-00804-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 01/30/2023]
Abstract
The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.
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Affiliation(s)
- Marie E. Kroeger
- grid.266683.f0000 0001 2184 9220Department of Microbiology, University of Massachusetts Amherst, Amherst, MA USA ,grid.148313.c0000 0004 0428 3079Present Address: Bioenergy and Biome Sciences, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Laura K. Meredith
- grid.134563.60000 0001 2168 186XSchool of Natural Resources and the Environment, University of Arizona, Tucson, AZ USA ,grid.134563.60000 0001 2168 186XBiosphere 2, University of Arizona, Tucson, AZ USA
| | - Kyle M. Meyer
- grid.170202.60000 0004 1936 8008Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA ,grid.47840.3f0000 0001 2181 7878Department of Integrative Biology, University of California–Berkeley, Berkeley, CA USA
| | - Kevin D. Webster
- grid.423138.f0000 0004 0637 3991Planetary Science Institute, Tucson, AZ USA
| | - Plinio Barbosa de Camargo
- grid.11899.380000 0004 1937 0722Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, SP Brazil
| | - Leandro Fonseca de Souza
- grid.11899.380000 0004 1937 0722Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, SP Brazil
| | - Siu Mui Tsai
- grid.11899.380000 0004 1937 0722Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, SP Brazil
| | - Joost van Haren
- grid.134563.60000 0001 2168 186XBiosphere 2, University of Arizona, Tucson, AZ USA ,grid.134563.60000 0001 2168 186XHonors College, University of Arizona, Tucson, AZ USA
| | - Scott Saleska
- grid.134563.60000 0001 2168 186XDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ USA
| | - Brendan J. M. Bohannan
- grid.170202.60000 0004 1936 8008Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA
| | - Jorge L. Mazza Rodrigues
- grid.27860.3b0000 0004 1936 9684Department of Land, Air and Water Resources, University of California, Davis, CA USA
| | - Erika Berenguer
- grid.9835.70000 0000 8190 6402Lancaster Environment Centre, Lancaster University, Lancaster, UK ,grid.4991.50000 0004 1936 8948Environmental Change Institute, University of Oxford, Oxford, UK
| | - Jos Barlow
- grid.9835.70000 0000 8190 6402Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Klaus Nüsslein
- grid.266683.f0000 0001 2184 9220Department of Microbiology, University of Massachusetts Amherst, Amherst, MA USA
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27
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Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil. Sci Rep 2021; 11:831. [PMID: 33437021 PMCID: PMC7804402 DOI: 10.1038/s41598-020-80840-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.
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28
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Nascimento Lemos L, Manoharan L, William Mendes L, Monteiro Venturini A, Satler Pylro V, Tsai SM. Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:651-655. [PMID: 32815317 DOI: 10.1111/1758-2229.12880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 05/10/2023]
Abstract
Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.
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Affiliation(s)
- Leandro Nascimento Lemos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Lokeshwaran Manoharan
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- National Bioinformatics Infrastructure Sweden (NBIS), Lund University, Lund, Sweden
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Andressa Monteiro Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Victor Satler Pylro
- Microbial Ecology and Bioinformatics Laboratory, Department of Biology, Federal University of Lavras (UFLA), Lavras, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
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29
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Berkelmann D, Schneider D, Hennings N, Meryandini A, Daniel R. Soil bacterial community structures in relation to different oil palm management practices. Sci Data 2020; 7:421. [PMID: 33257691 PMCID: PMC7705008 DOI: 10.1038/s41597-020-00752-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/29/2020] [Indexed: 11/26/2022] Open
Abstract
We provide soil bacterial 16 S rRNA gene amplicon and geochemical data derived from an oil palm plantation management experiment. The experimental design covered two different intensities of fertilizer application and weeding practices. We sampled the topsoil of 80 plots in total and extracted DNA and RNA. 16 S rRNA gene-derived and transcript-derived amplicons were generated and sequenced to analyse community composition and beta-diversity. One year after establishing the experiment, statistically significant differences of bacterial diversity or community composition between different treatments at entire (DNA-derived) and active (RNA-derived) community level were not detected. The dominant taxa belonged to Acidobacteriota and Actinobacteriota and were more abundant in the active community compared to the entire community. Similarly, the abundant genera Candidatus Solibacter and Haliangium were more abundant at active community level. Furthermore, clustering corresponding to the different sampling site locations was detected. Beta-diversity did not change among the treatments at DNA and RNA level. This dataset is of interest for related studies on the effect of altered management practices on soilborne communities.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Nina Hennings
- Department of Soil Science of Temperate Ecosystems, Buesgen Institute, University of Göttingen, Göttingen, Germany
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany.
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30
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Djemiel C, Goulas E, Badalato N, Chabbert B, Hawkins S, Grec S. Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota. Front Genet 2020; 11:581664. [PMID: 33193706 PMCID: PMC7652851 DOI: 10.3389/fgene.2020.581664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
The mechanical and chemical properties of natural plant fibers are determined by many different factors, both intrinsic and extrinsic to the plant, during growth but also after harvest. A better understanding of how all these factors exert their effect and how they interact is necessary to be able to optimize fiber quality for use in different industries. One important factor is the post-harvest process known as retting, representing the first step in the extraction of bast fibers from the stem of species such as flax and hemp. During this process microorganisms colonize the stem and produce hydrolytic enzymes that target cell wall polymers thereby facilitating the progressive destruction of the stem and fiber bundles. Recent advances in sequencing technology have allowed researchers to implement targeted metagenomics leading to a much better characterization of the microbial communities involved in retting, as well as an improved understanding of microbial dynamics. In this paper we review how our current knowledge of the microbiology of retting has been improved by targeted metagenomics and discuss how related '-omics' approaches might be used to fully characterize the functional capability of the retting microbiome.
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Affiliation(s)
- Christophe Djemiel
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Estelle Goulas
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Nelly Badalato
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Brigitte Chabbert
- Université de Reims Champagne Ardenne, INRAE, UMR FARE A 614, Reims, France
| | - Simon Hawkins
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Grec
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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31
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Monteiro DA, Fonseca EDS, Rodrigues RDAR, da Silva JJN, da Silva EP, Balieiro FDC, Alves BJR, Rachid CTCDC. Structural and functional shifts of soil prokaryotic community due to Eucalyptus plantation and rotation phase. Sci Rep 2020; 10:9075. [PMID: 32493970 PMCID: PMC7270125 DOI: 10.1038/s41598-020-66004-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/27/2020] [Indexed: 11/09/2022] Open
Abstract
Agriculture, forestry and other land uses are currently the second highest source of anthropogenic greenhouse gases (GHGs) emissions. In soil, these gases derive from microbial activity, during carbon (C) and nitrogen (N) cycling. To investigate how Eucalyptus land use and growth period impact the microbial community, GHG fluxes and inorganic N levels, and if there is a link among these variables, we monitored three adjacent areas for 9 months: a recently planted Eucalyptus area, fully developed Eucalyptus forest (final of rotation) and native forest. We assessed the microbial community using 16S rRNA gene sequencing and qPCR of key genes involved in C and N cycles. No considerable differences in GHG flux were evident among the areas, but logging considerably increased inorganic N levels. Eucalyptus areas displayed richer and more diverse communities, with selection for specific groups. Land use influenced communities more extensively than the time of sampling or growth phase, although all were significant modulators. Several microbial groups and genes shifted temporally, and inorganic N levels shaped several of these changes. No correlations among microbial groups or genes and GHG were found, suggesting no link among these variables in this short-rotation Eucalyptus study.
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Affiliation(s)
- Douglas Alfradique Monteiro
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo da Silva Fonseca
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | - Caio Tavora Coelho da Costa Rachid
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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32
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Lima JY, Moreira C, Nunes Freitas PN, Olchanheski LR, Veiga Pileggi SA, Etto RM, Staley C, Sadowsky MJ, Pileggi M. Structuring biofilm communities living in pesticide contaminated water. Heliyon 2020; 6:e03996. [PMID: 32462094 PMCID: PMC7240113 DOI: 10.1016/j.heliyon.2020.e03996] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/07/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
The wide use of pesticides in agriculture expose microbiota to stressful conditions that require the development of survival strategies. The bacterial response to many pollutants has not been elucidated in detail, as well as the evolutionary processes that occur to build adapted communities. The purpose of this study was to evaluate the bacterial population structure and adaptation strategies in planktonic and biofilm communities in limited environments, as tanks containing water used for washing herbicide containers. This biodiversity, with high percentage of nonculturable microorganisms, was characterized based on habitat and abiotic parameters using molecular and bioinformatics tools. According to water and wastewater standards, the physicochemical conditions of the tank water were inadequate for survival of the identified bacteria, which had to develop survival strategies in this hostile environment. The biodiversity decreased in the transition from planktonic to biofilm samples, indicating a possible association between genetic drift and selection of individuals that survive under stressful conditions, such as heating in water and the presence of chlorine, fluorine and agrochemicals over a six-month period. The abundance of Enterobacter, Acinetobacter and Pseudomonas in biofilms from water tanks was linked to essential processes, deduced from the genes attributed to these taxonomic units, and related to biofilm formation, structure and membrane transport, quorum sensing and xenobiotic degradation. These characteristics were randomly combined and fixed in the biofilm community. Thus, communities of biofilm bacteria obtained under these environmental conditions serve as interesting models for studying herbicide biodegradation kinetics and the prospects of consortia suitable for use in bioremediation in reservoirs containing herbicide-contaminated wastewater, as biofilters containing biofilm communities capable of degrading herbicides.
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Affiliation(s)
- Jhenifer Yonara Lima
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | - Cassiano Moreira
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | - Paloma Nathane Nunes Freitas
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | | | - Sonia Alvim Veiga Pileggi
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | - Rafael Mazer Etto
- Department of Chemistry, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | - Christopher Staley
- The Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States
| | - Michael Jay Sadowsky
- Department of Soil, Water, and Climate, The Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States
| | - Marcos Pileggi
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
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Muñoz-Arenas LC, Fusaro C, Hernández-Guzmán M, Dendooven L, Estrada-Torres A, Navarro-Noya YE. Soil microbial diversity drops with land-use change in a high mountain temperate forest: a metagenomics survey. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:185-194. [PMID: 31965701 DOI: 10.1111/1758-2229.12822] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Land-use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high-altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of bacteria, archaea and DNA virus in terms of effective number of species in high-altitude temperate oak and pine-oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land-use change. Archaea diversity was not affected by land-use change, but the bacterial diversity decreased with 45-55% when the oak forest was converted to arable land and 65-75% when the pine-oak forest was. Loss in bacterial diversity as a result of land-use change was positively correlated (R2 = 0.41) with the 10-25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land-use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine-oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity.
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Affiliation(s)
- Ligia C Muñoz-Arenas
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, Mexico
- Facultad de Ingeniería Ambiental, UPAEP Universidad, Puebla, Mexico
| | - Carmine Fusaro
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, Mexico
| | | | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS-Cinvestav, Ciudad de México, México
| | - Arturo Estrada-Torres
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Yendi E Navarro-Noya
- Cátedras Conacyt-Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, México
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Berkelmann D, Schneider D, Meryandini A, Daniel R. Unravelling the effects of tropical land use conversion on the soil microbiome. ENVIRONMENTAL MICROBIOME 2020; 15:5. [PMID: 33902736 PMCID: PMC8067294 DOI: 10.1186/s40793-020-0353-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/18/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry ("jungle rubber") and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia. RESULTS The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility- and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils. CONCLUSIONS Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility- and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany.
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Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe 2019; 26:283-295.e8. [PMID: 31415755 PMCID: PMC6716383 DOI: 10.1016/j.chom.2019.07.008] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/01/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023]
Abstract
Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.
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Affiliation(s)
- Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marc Beaudin
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Christina Baek
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
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Chernov TI, Zhelezova AD, Tkhakakhova AK, Bgazhba NA, Zverev AO. Microbiomes of Virgin Soils of Southern Vietnam Tropical Forests. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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37
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Pedrinho A, Mendes LW, Merloti LF, da Fonseca MDC, Cannavan FDS, Tsai SM. Forest-to-pasture conversion and recovery based on assessment of microbial communities in Eastern Amazon rainforest. FEMS Microbiol Ecol 2018; 95:5245175. [DOI: 10.1093/femsec/fiy236] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/12/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alexandre Pedrinho
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Luis Fernando Merloti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Mariley de Cassia da Fonseca
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Fabiana de Souza Cannavan
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
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